Merge pull request #94

*  - add basico to dependencies

*  - add simulate action

* Merge branch 'develop' into basico-simulate-button

Author: fbergmann

pyproject.toml

@@ -25,7 +25,9 @@ dependencies = [
     "python-libsbml",
     "matplotlib",
     "petab",
-    "qtawesome"
+    "qtawesome",
+    "copasi-basico",
+    "copasi-petab-importer"
 ]
 
 [build-system]

src/petab_gui/controllers/mother_controller.py

@@ -339,6 +339,12 @@ def setup_actions(self):
         # Recent Files
         actions["recent_files"] = self.recent_files_manager.tool_bar_menu
 
+        # simulate action
+        actions["simulate"] = QAction(
+            qta.icon("mdi6.play"), "Simulate", self.view
+        )
+        actions["simulate"].triggered.connect(self.simulate)
+
         # Filter widget
         filter_widget = QWidget()
         filter_layout = QHBoxLayout()
@@ -930,6 +936,34 @@ def _on_simulation_selection_changed(self, selected, deselected):
             y_axis_col="simulation"
         )
 
+    def simulate(self):
+        """Simulate the model."""
+        # obtain petab problem
+        petab_problem = self.model.current_petab_problem
+
+        # import petabsimualtor
+        from basico.petab import PetabSimulator
+        import basico
+
+        # report current basico / COPASI version
+        self.logger.log_message(f"Simulate with basico: {basico.__version__}, COPASI: {basico.COPASI.__version__}", color="green")
+
+        import tempfile
+
+        # create temp directory in temp folder:
+        with tempfile.TemporaryDirectory() as temp_dir:
+            # settings is only current solution statistic for now:
+            settings = {'method' : {'name': basico.PE.CURRENT_SOLUTION}}
+            # create simulator
+            simulator = PetabSimulator(petab_problem, settings=settings, working_dir=temp_dir)
+
+            # simulate
+            sim_df = simulator.simulate()
+
+        # assign to simulation table
+        self.simulation_controller.overwrite_df(sim_df)
+        self.simulation_controller.model.reset_invalid_cells()
+
     def _schedule_plot_update(self):
         """Start the plot schedule timer."""
         self._plot_update_timer.start()

src/petab_gui/views/main_view.py

@@ -180,6 +180,7 @@ def setup_toolbar(self, actions):
         tb.addAction(actions["delete_row"])
         tb.addAction(actions["add_column"])
         tb.addAction(actions["delete_column"])
+        tb.addAction(actions["simulate"])
         tb.addWidget(spacer)
         tb.addWidget(actions["filter_widget"])
 

src/petab_gui/views/task_bar.py

@@ -91,6 +91,7 @@ def __init__(self, parent, actions):
         self.menu.addSeparator()
         # Reset Model
         self.menu.addAction(actions["reset_model"])
+        self.menu.addAction(actions["simulate"])
         self.menu.addSeparator()
         # Settings
         self.menu.addAction(actions["settings"])